Some complexities in interpreting apparent effects of hitchhiking: a commentary on Gompert, Feder & Nosil (2021)

We write to address recent claims by Gompert et al. (2021) about the potentially important and underappreciated phenomena of “indirect selection”, the observation that neutral regions may be affected by natural selection. We argue both that this phenomenon – generally known as genetic hitchhiking – is neither new nor poorly studied, and that the patterns described by the authors have multiple alternative explanations.

The use of carefully planned board work to support the productive discussion of multiple student responses in a Japanese problem-solving lesson

In this paper, we analyse a grade 8 (age 13–14) Japanese problem-solving lesson involving angles associated with parallel lines, taught by a highly regarded, expert Japanese mathematics teacher. The focus of our observation was on how the teacher used carefully planned board work to support a rich and extensive plenary discussion (neriage) in which he shifted the focus from individual mathematical solutions to generalised properties. By comparing the teacher’s detailed prior planning of the board work (bansho) with that which he produced during the lesson, we distinguish between aspects of the lesson that he considered essential and those he treated as contingent. Our analysis reveals how the careful planning of the board work enabled the teacher to be free to explore with the students the multiple alternative solution methods that they had produced, while at the same time having a clear overall purpose relating to how angle properties can be used to find additional solution methods. We outline how these findings from within the strong tradition of the Japanese problem-solving lesson might inform research and teaching practice outside of Japan, where a deep heritage of bansho and neriage is not present. In particular, we highlight three prominent features of this teacher’s practice: the detailed lesson planning in which particular solutions were prioritised for discussion; the considerable amount of time given over to student generation and comparison of alternative solutions; and the ways in which the teacher’s use of the board was seen to support the richness of the mathematical discussions.

Complex regulation of Gephyrin splicing is a determinant of inhibitory postsynaptic diversity

Gephyrin (GPHN) regulates the clustering of postsynaptic components at inhibitory synapses and is involved in pathophysiology of neuropsychiatric disorders. Here, we uncover an extensive diversity of GPHN transcripts that are tightly controlled by splicing during mouse and human brain development. Proteomic analysis reveals at least a hundred isoforms of GPHN incorporated at inhibitory Glycine and GABA-A receptors containing synapses. They exhibit different localization and postsynaptic clustering properties, and altering the expression level of one isoform is sufficient to affect the number, size, and density of inhibitory synapses in cerebellar Purkinje cells. Furthermore, we discovered that splicing defects reported in neuropsychiatric disorders are carried by multiple alternative GPHN transcripts, demonstrating the need for a thorough analysis of the GPHN transcriptome in patients. Overall, we show that alternative splicing of GPHN is an important genetic variation to consider in neurological diseases and a determinant of the diversity of postsynaptic inhibitory synapses.

In silico evaluation of the interaction between ACE2 and SARS-CoV-2 Spike protein in a hyperglycemic environment

The worse outcome of COVID-19 in people with diabetes mellitus could be related to the non-enzymatic glycation of human ACE2, leading to a more susceptible interaction with virus Spike protein. We aimed to evaluate, through a computational approach, the interaction between human ACE2 receptor and SARS-CoV-2 Spike protein under different conditions of hyperglycemic environment. A computational analysis was performed, based on the X-ray crystallographic structure of the Spike Receptor-Binding Domain (RBD)-ACE2 system. The possible scenarios of lysine aminoacid residues on surface transformed by glycation were considered: (1) on ACE2 receptor; (2) on Spike protein; (3) on both ACE2 receptor and Spike protein. In comparison to the native condition, the number of polar bonds (comprising both hydrogen bonds and salt bridges) in the poses considered are 10, 6, 6, and 4 for the states ACE2/Spike both native, ACE2 native/Spike glycated, ACE2 glycated/Spike native, ACE2/Spike both glycated, respectively. The analysis highlighted also how the number of non-polar contacts (in this case, van der Waals and aromatic interactions) significantly decreases when the lysine aminoacid residues undergo glycation. Following non-enzymatic glycation, the number of interactions between human ACE2 receptor and SARS-CoV-2 Spike protein is decreased in comparison to the unmodified model. The reduced affinity of the Spike protein for ACE2 receptor in case of non-enzymatic glycation may shift the virus to multiple alternative entry routes.

A Highly Sensitive GFP Activation Assay for Detection of DNA Cleavage in Cells

CRISPR/Cas9 nucleases hold great potential for gene therapy, but they frequently induce unwanted off-target cleavage. We previously developed a GFP activation assay for detection of DNA cleavage in cells. Here, we demonstrate two novel applications of this assay. First, we use this assay to confirm off-target cleavage that cannot be detected by targeted deep sequencing in cells before. Second, we use this approach to detect multiple alternative PAMs recognized by SpCas9. These noncanonical PAMs are associated with low cleavage activity, but targets associated with these PAMs must be considered as potential off-target sites. Taken together, the GFP activation assay is a powerful platform for DNA cleavage detection in cells.

Local and collective transitions in sparsely-interacting ecological communities

Interactions in natural communities can be highly heterogeneous, with any given species interacting appreciably with only some of the others, a situation commonly represented by sparse interaction networks. We study the consequences of sparse competitive interactions, in a theoretical model of a community assembled from a species pool. We find that communities can be in a number of different regimes, depending on the interaction strength. When interactions are strong, the network of coexisting species breaks up into small subgraphs, while for weaker interactions these graphs are larger and more complex, eventually encompassing all species. This process is driven by emergence of new allowed subgraphs as interaction strength decreases, leading to sharp changes in diversity and other community properties, and at weaker interactions to two distinct collective transitions: a percolation transition, and a transition between having a unique equilibrium and having multiple alternative equilibria. Understanding community structure is thus made up of two parts: first, finding which subgraphs are allowed at a given interaction strength, and secondly, a discrete problem of matching these structures over the entire community. In a shift from the focus of many previous theories, these different regimes can be traversed by modifying the interaction strength alone, without need for heterogeneity in either interaction strengths or the number of competitors per species.

Edible nanocoatings: potential food applications, challenges and safety regulations

Purpose This review discusses the concept of edible nanocoatings (ENCs), the biomaterials used in the coating matrices, techniques of coating development, applications, challenges and safety regulations associated with nanotechnology in food products. These ENCs are capable of imparting increased shelf life, improved appearance, better physiological qualities and bioactive potentials such as antimicrobial and antioxidant properties. ENCs can be developed using the layer-by-layer method which forms multiple alternative layers adhered together primarily by electrostatic interactions. Design/methodology/approach Various keywords such as edible coatings (ECs), safety aspects and nanocoatings were used to search the literature from Google Scholar, Research Gate, ScienceDirect, Springer Link, Taylor and Francis and PubMed. After searching enough literature, 113 articles and research papers were examined, which provides the updated overview of different aspects of edible nano-coatings. Findings Consumers today are very much aware of the food quality and its safety. They demand food products with longer shelf life, which are minimally processed with natural or no preservatives. ECs based on biopolymers is an alternative technique, which is biodegradable and can be consumed as such without posing any safety risks. The emergence of nanotechnology in food processing has provided new insights to develop ECs at the nanoscale with improved mechanical and barrier properties Originality/value ECs are beneficial to consumers and to the environment. ECs have generated significant attention over years as an alternative to fossil-based plastics, considering their renewable and biodegradable features